4KTQ

BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM T. AQUATICUS BOUND TO A PRIMER/TEMPLATE DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

Li, Y.Korolev, S.Waksman, G.

(1998) EMBO J 17: 7514-7525

  • DOI: 10.1093/emboj/17.24.7514
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structures of two ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA and dideoxycytidine triphosphate, and that of a binary complex of the same enzyme with a primer/template ...

    The crystal structures of two ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA and dideoxycytidine triphosphate, and that of a binary complex of the same enzyme with a primer/template DNA, were determined to a resolution of 2.3, 2.3 and 2.5 A, respectively. One ternary complex structure differs markedly from the two other structures by a large reorientation of the tip of the fingers domain. This structure, designated 'closed', represents the ternary polymerase complex caught in the act of incorporating a nucleotide. In the two other structures, the tip of the fingers domain is rotated outward by 46 degrees ('open') in an orientation similar to that of the apo form of Klentaq1. These structures provide the first direct evidence in DNA polymerase I enzymes of a large conformational change responsible for assembling an active ternary complex.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Campus Box 8231, 660 South Euclid Avenue, St Louis, MO 63110, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (LARGE FRAGMENT OF DNA POLYMERASE I)A539Thermus aquaticusMutation(s): 0 
Gene Names: TAQpolApol1
EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus)
Explore P19821 
Go to UniProtKB:  P19821
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')B12N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')C13N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.842α = 90
b = 110.842β = 90
c = 90.843γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1998-09-09 
  • Released Date: 1999-01-13 
  • Deposition Author(s): Li, Y., Waksman, G.

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance